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In clause (ii) of Meyer’s definition, it is perhaps sufficient to observe that he conflates the undebated idea of common ancestry in general with the actual debate about whether it is possible to identify a single universal common ancestor. Woese’s work (e.g. [7]), to which Scott was alluding in the forum that Meyer mentions, contributes to the latter debate. There is no reason not to sketch Woese’s basic idea in a pre-university biology class. However, it would be scientifically inappropriate and pedagogically irresponsible to pretend that it challenges the common ancestry of primates, tetrapods, or eukaryotes, or that it constitutes evidence for a special creation of the three domains, or that it is anything but a necessary refinement of the idea of common ancestry.

(Scott and Branch in "Teaching the controversy: response to Langen and to Meyer")

Recently Carl Woese has corrected these interpretations so this should be the end of it. But will it?

Woese scoffs at Meyer’s claim when I call to ask him about the paper. “To say that my criticism of Darwinists says that evolutionists have no clothes,” Woese says, “is like saying that Einstein is criticizing Newton, therefore Newtonian physics is wrong.” Debates about evolution’s mechanisms, he continues, don’t amount to challenges to the theory. And intelligent design “is not science. It makes no predictions and doesn’t offer any explanation whatsoever, except for ‘God did it.’”

Dembski 2002

There is a question about the extent of evolution, but that is a question being raised by non-ID scientists. Carl Woese in the Proceedings of the National Academy of Sciences just a few weeks ago published a piece where he explicitly rejects common descent. What ID proponents want is to teach is the evidence for evolution as well as whatever evidence places limits on evolutionary change (like Carl Woese’s idea of lateral gene transfer). Scott and Branch are here merely playing on fears of school boards and educators.

One may object to Woese’s definition of common descent since Darwin himself seems to accept the possibility of multiple common ancestors. But Dembski misses the point namely that Woese does not reject common descent as much as argues that there was a pre-Darwinian period and that there are three common ancestors.

In a later paper Woese corrects this oversight

Where did this doctrine come from? Why, Darwin, of course: didn’t he say that all life stems from a single primordial form? Indeed he did. But look at the context and way in which Darwin addresses the issue in Origin of Species. Herein we read (12): “… [we may infer] that all the organic beings which have ever lived on this earth may be descended from some one primordial form. But this inference is chiefly grounded on analogy and it is immaterial whether or not it be accepted. No doubt it is possible, as Mr. G. H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so we may conclude that only a very few have left modified descendants.”

(C. R. Woese A New Biology for a New Century Microbiol. Mol. Biol. Rev., June 1, 2004; 68(2): 173 - 186. )

Meyer 2004

“Meyer claimed a recent Woese article in Microbiology and Molecular Biology Reviews argued that “the Darwinian emperor has no clothes”. So Ratliff called Woese. Here’s the reply:”

Woese scoffs at Meyer’s claim when I call to ask him about the paper. “To say that my criticism of Darwinists says that evolutionists have no clothes,” Woese says, “is like saying that Einstein is criticizing Newton, therefore Newtonian physics is wrong.” Debates about evolution’s mechanisms, he continues, don’t amount to challenges to the theory. And intelligent design “is not science. It makes no predictions and doesn’t offer any explanation whatsoever, except for ‘God did it.’”

Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.

(C. R. Woese A New Biology for a New Century Microbiol. Mol. Biol. Rev., June 1, 2004; 68(2): 173 - 186. )

Woese describes a Darwinian threshold:

That stage is the Darwinian threshold, the critical point before which HGT dominates the evolutionary dynamic and after which it does not—thus allowing stable organismal genealogies to emerge (63). Only then can living systems finally be conceptualized in discreet, idiosyncratic species terms. Note the phrase “begins to become” above: if only one of the major evolving cell designs were to cross its Darwinian threshold, tree representation would appear to be appropriate because that one lineage (only) would be distinguishable from all the rest, despite the fact that the others did not yet exist as discrete stable lineages, having not yet undergone Darwinian transitions of their own.

(C. R. Woese A New Biology for a New Century Microbiol. Mol. Biol. Rev., June 1, 2004; 68(2): 173 - 186. )

Darwinian common descent

It has been suggested that horizontal gene transfer (HGT) is the ‘‘essence of phylogeny.” In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.

I think we can make this a bit simplier and state in the stereotype of common descent used by evolution deniers is that once upon a time – poof – there formed a single cell and that cell is the sole common ancestor of all life on earth.

The phrase “common descent” in reality does not require such a hypothesis. First of all, the common ancestor could have easily have been a population of cells and not a single cell. This does not require independent abiogenesis events.

Second of all it is possible that the evolution of replicators (DNA, RNA, and/or whatever) might have already exist before they first started to aquired cell membranes. If that is true than evolution started before the first cell which makes the idea that one cell as the common ancestor as fairly silly. In this idea the replicators can already have evolved differences before the evolution of the cell and thus Woese’s idea that life on Earth is descended from “three distinctly different cell types”

It was only a couple weeks ago that some creationist posting here brought up Woese’s comments here in an effort to attack evolutionary theory, going so far as to provide a link to Woese’s complete text (which clearly shows Woese’s absolutely unsurprising acceptance of evolutionary theory).

Will references to Woese’s comments dry up, I wonder? I wouldn’t bet it on it.

About a year ago I informed Woese that anti-evolutionists were misrepresenting his papers to imply that he thought modern life had multiple origins and that modern origanisms were not united by a common genetic history. He was perturbed, to put it mildly. I asked if the following was his view:

The three domains of life originated, somewhat independently, from the same pre-cellular pool which was undergoing massive lateral transfer of genetic information. You do not challenge common ancestry per se but rather the concept that there was a single common ancestor cell or organism that gave rise to the three cellular domains of life?

Woese affirmed that was correct and that “ancestry is in a sense common”, but suggested that communal is a better choice of words than common, since he sees common ancestry as implying strict linear, vertical inheritance.

Mostly Woese is trying to argue against the widely held caricature of common descent that all of life descended from a single ‘bacterium’ of sorts. His hypothesis is really about the nature of the last common ancestor, not about its existence. The LCA was a gene pool, probably pre-cellular, pre-membranes, dominated by horizontal rather than vertical inheritance. Woese’s view is in fact much more in line with the way we think of common ancestry in metazoans, mammals, etc. where a ‘common ancestor’ of multiple species is a population of organisms actively exchanging genes in a communal gene pool.

Do you really think that the last common ancestor/last common “gene pool” of bacteria and archaea was actually pre-cellular/pre-membrane? Don’t things like homologous secretion systems and the (membrane-bound) F1F0, A1A0, and V1V0-ATPases argue against that?

(Or, you might be saying that the first replicators were pre-cellular, pre-membrane, which seems much more likely. There is a long distance between the first noncellular replicators and the first cells, and probably a long distance between the first cells and the LCA. All IMVHO of course.)

Do you really think that the last common ancestor/last common “gene pool” of bacteria and archaea was actually pre-cellular/pre-membrane?

In the above I was just paraphrasing Woese’s view as I understand it from his papers and my conversations with him and Norm Pace. To be honest, I am skeptical of Woese’s hypothesis, though I think it is possible and consistent with what we know now. However, Woese’s views are not well-accepted by any means. There are many who question the dominance of HGT and think that many if not most instances of HGT are statistical artefacts (e.g., see the Caetano-Anollés article linked in the initial post and Glansdorff 2000 ). Woese has largely based his hypothesis on the apparent HGT events among aminoacyl-tRNA synthetases, but those phylogenies are unstable and plagued by things like long-branch attraction and GC bias that leaks through into the protein sequences. There are people actively working on ways to get around these problems (like Steve Freeland and Rob Knight) and they may soon come up with some solid answers in the synthetase case anyway. One of my problems with Woese’s views is that I’m unaware of any good tests he has proposed. One way of tackling this, I think, is to figure out phylogenetically how many HGT events are necessary to reconcile the best tree with the data (after statistical noise has been accounted for). Mike Steel and some others are working on the mathematics of this surprisingly difficult phylogenetic issue (reticulate trees). If we can estimate the minimum number of HGT events that occurred among the three domains early in evolution, we could get a handle on the rate of early HGT and see if it is actually much higher than the rates of HGT we see now among modern unicellulars (as Woese proposes).

Don’t things like homologous secretion systems and the (membrane-bound) F1F0, A1A0, and V1V0-ATPases argue against that?

I think there is a case there, but that depends on how prevalent HGT was in early evolution. Woese would likely argue that those are homologous because they were inherited via HGT, possibly after the three domains had largely crossed what he calls the “Darwinian threshold.” You probably know better than I – how consistent are phylogenies of those proteins with the “classical” rooted universal phylogeny of (bacteria, (eukaryae, archaea))? Much of Woese’s argument pivots on pre-membrane evolution, so looking at phylogenies of membrane associated proteins may be another way to test his hypothesis.

I do know that the ATPases follow the (bacteria (archaea, eukaryotes)) pattern (F, (A, V)), although there is some lateral transfer of these that has been detected (V-ATPases in bacteria IIRC). I don’t know about secretion systems offhand, just that the sec/Type II system is shared (IIRC).